Importance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy

Figures & data

Table 1 Molecular Analysis of NDM-Kpn Clinical Isolates

Isolate	Hospital^a	Source	Genetic Determinants			Typing
			Beta-Lactam	Additional Resistance Genes	Plasmid Replicon	ST^b	Cluster^c
NDM-Kpn-1	H-1	Rectal swab	blaNDM-1, blaSHV-107	aac(6)-Ib, fosA, oqxB, sul1, dfrA14	colRNAI, IncFIA(HI1)	11	2
NDM-Kpn-2	H-2	Rectal swab	blaNDM-1, blaSHV-11	fosA, oqxB, sul1, dfrA14	colRNAI, IncL/M(pMU407)	11	2
NDM-Kpn-3	H-3	Wound swab	blaNDM-1, blaOXA-48, blaSHV-28, blaCMY-6, blaCTX-M-15	aac(6)-Ib3, rmtC, fosA, oqxA, oqxB, sul2, dfrA14	IncA/C2, IncL/M(pOXA-48), IncR	15	1
NDM-Kpn-4	H-3	Wound swab	blaNDM-1, blaOXA-1, blaOXA-9, blaSHV-81, blaTEM-1A, blaCTX-M-15	aph(3ʹ)-VI, aac(6ʹ)-Ib, aac(6ʹ)-Ib3, aadA1, armA, aac(6ʹ)-Ib-cr, fosA_3, fosA_5, msr(E), mph(A), catB3, qnrS1, oqxA, oqxB, ARR-3, sul1, sul2 dfrA5	IncFIB(pQIL), IncR	147	–
NDM-Kpn-5	H-3	Wound swab	blaNDM-5, blaOXA-9, blaSHV-26, blaTEM-1C, blaCTX-M-15	aph(3ʹ)-VI, aac(6ʹ)-Ib, aadA1, aph(3ʹ)-Ia, armA, fosA_3, fosA_5, msr(E), mph(A), mph(E), catA1, qnrS1, oqxA, oqxB, sul1, sul2, tet(A), dfrA5	IncFIB(Mar), IncHI1B	383	5
NDM-Kpn-6	H-3	Blood	blaNDM-1, blaOXA-48, blaSHV-55, blaCMY-6, blaCTX-M-15	aac(6ʹ)-Ib3, rmtC, fosA, oqxA, oqxB, sul1, sul2, dfrA14	IncA/C2, IncL/M(pOXA-48), IncR	15	1
NDM-Kpn-7	H-4	Wound swab	blaNDM-1, blaOXA-1, blaOXA-10, blaSHV-28, blaTEM-1B, blaCTX-M-15	aph(6)-Id, aac(6ʹ)-II, aph(3ʹ)-VI, aac(3ʹ)-IIe, aac(6ʹ)-Ib-cr, aph(3”)-Ib, fosA_3, catB3, qnrB1, qnrS1, oqxA, oqxB, sul1, sul2, tet(A), dfrA14	colRNAI, IncFIB(pQIL)	307	–
NDM-Kpn-8	H-3	Wound swab	blaNDM-1, blaOXA-48, blaSHV-106, blaCMY-6, blaCTX-M-15	aac(6ʹ)-Ib3, rmtC, fosA, oqxA, oqxB, sul2, dfrA14	IncA/C2, IncL/M(pOXA-48)	15	1
NDM-Kpn-9	H-3	Rectal swab	blaNDM-1, blaOXA-48, blaCMY-6, blaSHV-148, blaTEM-1B, blaCTX-M-14b	aph(6)-Id, aac(3ʹ)-IIa, aac(6ʹ)-Ib3, aph(3ʹ)-VIb, aph(3”)-Ib, rmtC, mph(A), fosA_3, catA1, oqxA, oqxB, sul1, tet(A)	IncA/C2, IncR, IncL/M(pOXA-48)	4853	–
NDM-Kpn-10	H-3	Rectal swab	blaNDM-1, blaOXA-48, blaCMY-6, blaSHV-148, blaOXA-9, blaTEM-1C, blaCTX-M-15, blaCTX-M-14b	aph(6)-Id, aac(6ʹ)-Ib, aph(3ʹ)-VI, rmtC, mph(A), aac(3ʹ)-IIe, aac(6ʹ)-Ib-cr, aph(3”)-Ib, fosA_3, catA1, qnrS1, oqxA, oqxB, sul1, sul2, tet(A)	IncA/C2, IncL/M(pOXA-48)	383	5
NDM-Kpn-11	H-3	Wound swab	blaNDM-1, blaSHV-155, blaOXA-1, blaTEM-1B, blaCTX-M-15, blaSCO-1	aph(6)-Id, aac(3ʹ)-IIa, addA1, aac(6ʹ)-Ib-cr, fosA_3, catB3, qnrB1, oqxA, oqxB, sul1, sul2, tet(A), dfrA15	IncFIB(pQIL)	17	–
NDM-Kpn-12	H-5	Blood	blaNDM-1,blaOXA-1,blaOXA-9,blaSHV-11,blaTEM1A,blaCTX-M-15	aac(6ʹ)-Ib, aph(3ʹ)-VI, aph(3ʹ)-Ia, aadA1, armA, msr(E), mph(A), mph(E), aac(6ʹ)-Ib-cr, fosA_5, catB3, qnrS1, oqxA, oqxB, ARR-3, sul1, sul2, dfrA5	colRNAI, IncFIB(pQIL), IncR	147	–
NDM-Kpn-13	H-6	Central venous catheter	blaNDM-1, blaOXA-48, blaSHV-148, blaCTX-M-14b	aph(6)-Id, aph(3ʹ)-Ib, rmtF, mph(A), fosA_3, fosA_5, catA1, qnrB1, oqxA, oqxB, AAR-2, tet(A)	IncFIB(pQIL), IncL	383	4
NDM-Kpn-14	H-4	Rectal swab	blaNDM-1, blaOXA-1, blaSHV-11, blaTEM-1B, blaCTX-M-15	addA1, aac(6ʹ)-Ib-cr, fosA_3, fosA_5, catB3, qnrB1, oqxA, oqxB, sul1, dfrA15	IncFIB(pQIL)	147	3
NDM-Kpn-15	H-6	Blood	blaNDM-1, blaOXA-48, blaSHV-148, blaCTX-M-14b	aph(6)-Id, aph(3ʹ)-Ib, rmtF, mph(A), fosA_3, fosA_5, catA1, qnrB1, oqxA, oqxB, AAR-2, tet(A)	IncFIB(pQIL), IncL	383	4
NDM-Kpn-16	H-4	Sputum	blaNDM-1, blaOXA-1, blaSHV-81, blaTEM-1B, blaCTX-M-15	addA1, aac(6ʹ)-Ib-cr, fosA_3, fosA_5, catB3, qnrB1, oqxA, oqxB, sul1, dfrA1_5, dfrA1_10	IncFIB(pQIL)	147	3
NDM-Kpn-17	H-7	Rectal swab	blaNDM-1, blaOXA-10, blaSHV-2, blaSHV-187, blaTEM-1A	aac(6ʹ)-II, aph(3ʹ)-VI, acc(3)-IId, aadA16, aac(6ʹ)-Ib-cr, fosA_3, floR_2, qnrB6, qnrS1, oqxA, oqxB, ARR-3, sul1, sul2, tet(A), tet(D), dfrA27	IncFIB(pQIL), IncR	29	–

Notes: ^aStrains collected from seven different hospitals in Rome (H-1 to H-7); ^bsequence type (ST) identified by MLST; ^ccluster types (CT-1 to CT-5) identified using cgMLST method.

Abbreviations: CT, cluster type; H, hospital; NDM-Kpn, New Delhi metallo-β-lactamase producing Klebsiella pneumoniae; ST, sequence types; cgMLST, core genome multilocus sequence typing.

Figure 1 Minimum spanning tree based on cgMLST analysis of 17 NDM-producing K. pneumoniae isolates (NDM-Kpn-1 to NDM-Kpn-17), showing 5 cluster types numbered consecutively (1 and 5). Each circle represents an allelic profile, ie sequence type (ST), based on sequence analysis of up to 2358 target genes. Cluster types consist of closely related genotypes (≤ 15 allele differences). The numbers on the connecting lines illustrate the numbers of target genes with different alleles.